Function that simulates a stochastic trajectory with the Gillespie algorithm given certain experimental conditions and a parameter vector, and computes the distance between the simulation and the experimental data
simulateAndComputeDistance.RdFunction that simulates a stochastic trajectory with the Gillespie algorithm given certain experimental conditions and a parameter vector, and computes the distance between the simulation and the experimental data
Usage
simulateAndComputeDistance(
e,
param,
parMap = parMap,
Phi = Phi,
parameters_from_expressions = parameters_from_expressions,
nStochSim = nStochSim,
reactions = compiled_reactions,
distance = distance
)Arguments
- e
an experiment
- param
a named parameter vector
- parMap
a function that translates ABC variables (parABC) into something the model will accept.
- Phi
Volume
- parameters_from_expressions
a vector of evaluated expressions
- nStochSim
number of stochastic simulations to average over
- reactions
a list that encodes the reactions for GillespieSSA2
- distance
a user supplied function that calculates a distance between simulation and data with an interface of distance(simulation, data, errVal), where errVal is an estimate of the measuremnet noise (e.g. standard deviation), if needed by the function.